Why would they not reconcile? I believe that hand-held GPS devices are only accurate to the specifications of the receiver chips. These are not military grade chips being used. And as such small errors may be induced over many data points. Think of them as rounding errors. Additionally, different GPS units were used to track the PCT and each unit has it's own calibration independent of the other.
How Ben Go got to a perfect reconciliation between start and finish is not clear to me. And let me say that Halfmile' data, based on Jim's post vs. the map's start and finish elevation is only off by 35' making it incredibly accurate. Consider, according to Jim's sheet, that you climbed 92.6931 miles and descended 92.5018 miles to be off by only 35' is really reconciliation as it is only 0.003579%.
Halfmile, YOU ROCK!
Thumper